What bike and what size wheel are you mounting the fenders to?
I have 4 bikes that have these fenders and the only way I possibly get that much extra say sticking out is with the fenders meant for a 700c wheel mounted on my Hardrock with the 26" wheels (commuter with skinnier slicks).

I use BMX style pinned platforms instead of clipless and have never had an issue with clearance.
Perhaps it's the geometry and headtube angle of your bike that is the major contributor to clearance issues.

Trimming excess stay sticky-outage (technical term) shouldn't cause a problem and my help prevent leg perforations in a crash.
Just make sure you file down any sharp edges.

The only other thing I can think of right now is you probably will need to broaden and extend the mudflap section a bit if you will be having very wet conditions on your route, as sometimes the water will still spray a bit of your feet with the setup as is.